Replace the return with a function (push, unshift, splice, as examples) that builds up a temporary array that you return.

I would probably build it in two parts -- one that iterates over all of @data, one line at a time, and the other part that handles one line at a time. I might even put the part that iterates over @data back into the code that is calling your sub (perhaps with map or something similar).

Your code is basically selecting a group of lines, and then transforming them. To me that says something along these lines (see grep and map):

my @output = map {
        doTransformation( $_ );
    }
    grep {
        shouldSelectData( $_ );
    }
    @data;
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